Category Archives: Tutorials

Hello Archaeopy! We will be releasing our Geophysical challenge two next week! To get you ready for this challenge, here is the complementary tutorial covering numpy arrays. We have discussed numpy before in previous posts, but since it is the fundamental package for handling our data, we thought it would be important to cover the numpy basics once more. Much of this tutorial will be taken from the tutorial on the official numpy webpage. Check it out for further information.

Why numpy?

Numpy's main object is the multidimensional array. Consider geophysical data: we have positional coordinates (x and y) and at least one value (z). There are many ways we can handle this information (e.g. xyz file, grd file, as profiles). Numpy arrays are efficient for handling, storing, and manipulating large datasets.

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It has been a few weeks since we have posted our first geophysical challenge. We thought to create a tutorial post for the challenge to help you along! First things first, you will need to download the data for this challenge. Save this data to the same folder you will be saving your python challenge 1 script to. Now open Spyder. We have provided a step-by-step tutorial with information about each step, to help you along.

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Hello! This guide will help you to get started with ArchaeoPY. This will cover installations you will need, how to utilise our repository, and how to get going running code. Stay tuned for Python Basics and Coding Basics guides! We are just in the process of putting them into a more GitHub/external-user-friendly form from our ipython notebook server.

1. Getting Started: Anaconda:

First things first, you will need Python installed on your computer. We recommend running Python 2.7 through Anaconda: http://continuum.io/downloads

"""
Program to Open a file and print the contents line by line
"""
#Sets the path and Filename that you want to Open.
filename = 'data/MultipleLineText.txt'
#Opens the file defined by filename, 'r' refers to the file as being opened to read
f = open(filename, 'r')
# *Loop* For each Line in the file 'f' does whatever is inside the loop
for line in f:
#The indentation means were inside the loop
#Prints the line
print line
#Closes the file 'f'
f.close()

I'm hoping the comments are detailed enough to explain what this code does

Reading and Doing Something

Suppose we have some X, Y, C1, C2 data in a comma delimited text file with a Header line and we want to calculate the mean, min, max and standard deviation.

This gives us the option to try out modules. The code and data is available here

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The 10th International conference on Archaeological Prospection in Vienna involved a small but significant discussion about Open Software. This has continued on Twitter and I've committed myself to helping people start writing OpenSource software in Python.

I've chosen the Python Programming Language, partly because its one i have a working knowledge of but more importantly because it's inherently user readable. We have to remember that primarily we're Scientists, Archaeologists & Geophysicists, not Programmers and by using Python we can concentrate on what we want to happen to our data rather than how to tell the computer what you want to happen to the data.

Installing Python

To Get started with Python you'll need an implementation of Python on your computer. Python is Cross-Platform (It will work on windows, linux, mac ...) but the method of installing it on different platforms can be very different.

I've traditionally used PythonXY and Spyder on Windows and Mac Systems. For the purposes of this introduction i'm going to recommend Anoconda because its entirely Cross-Platform and therefore we should all encounter the same issues at the same time.

The installation method is slightly different between different operating systems but the Anaconda Support documents are detailed enough, i think.

It's only during the Writing of this post that i've encountered Anaconda. This was very easy to install on my mac and includes 64Bit support unlike PythonXY. I'm going to try using both Anaconda and PythonXY to see if they both work seamlessly..

Keeping Track of Code Changes

I found one of the hardest and most frustrating things when i started writing code to process my Geophysical data was i changed it so much from day to day it was impossible to know how i'd created a particular dataset. I should have used a revision control system from the start but didn't so i'm going to recommend you do.

I've chosen to use EasyMercurial because its the one favoured by SoftwareCarpentry and completely cross platform, some instructions are available here.

Getting started with Spyder

To start writing some code open up Spyder:

Opening Spyder on Mac OSX

Opening Spyder on Windows

I Like to think Spyder is relatively simple but to the Non-Programmer it probably makes about as much sense as digging does to me. Hence the image below...

This looks the same on whatever Operating System your running and you'll probably find i flick between Mac, Windows and Ipython.

Writing Some Code

Well we've done the boring stuff and got everything we need installed. Now to write some code.

Create a New file in Spyder and you should see something similar to this:

the """ and # denote that the text is a comment and should not be 'run' as code. On a new line underneath the MetaData Comment section type

print ("Hello World")

Run the Code by pressing F5, save the file as something sensible within your EasyMercurial repository, and accept the default runtime options. You should see the following:

You've just written your first Python program. Its not particularly useful but is good step along the way.

I'm going to write another post soon with more useful python programming (reading, doing something, saving data) and start to move my tools and libraries into ArchaeoPY. For now i'd recommend looking at the information and tutorials on SoftwareCartpentry

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Spyder is a great python development environment available through Python XY on Windows. Getting it to run on Mac OS X is a little more complicated however. You can't just download a binary image (.dmg), you need to compile the code from source.

The easiest way i found is to use MacPorts which comes with a package installer (think setup file).

install py-spyder - This should include most required dependencies including python 2.7, numpy etc.. and because of this it takes a while

then open spyder from the terminal

As i said before most required python libraries should be installed using this method but not everything included with python xy. If you find you need a module that is not installed chances are you'll be able to find it on macports. If unsure ask and google.